Contacts of the strand formed by residues 180 - 183 (chain E) in PDB entry 1PPE


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with MET 180 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  THR      3.6    23.6    -      -       -      +
     99E  LEU      3.7    18.4    -      -       -      +
    100E  ASN*     3.8     7.2    -      -       -      -
    101E  ASN      6.2     0.2    -      -       -      +
    165E  ASP*     4.7     7.6    -      -       -      +
    175E  GLN      3.6    12.1    -      -       -      +
    176E  ILE*     4.0    12.7    -      -       +      +
    177E  THR*     3.4    51.6    +      -       +      +
    178E  SER      3.3     1.7    -      -       -      +
    179E  ASN*     1.3    84.8    -      -       +      +
    181E  PHE*     1.3    64.2    +      -       -      +
    215E  TRP*     3.9    19.3    -      -       +      +
    227E  VAL*     3.8    17.9    -      -       +      -
    228E  TYR      3.1     9.0    -      -       -      +
    229E  THR*     5.4     0.7    -      -       -      -
    230E  LYS*     4.3     7.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 181 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162E  ILE*     3.9    39.5    -      -       +      -
    163E  LEU      5.3     1.6    -      -       -      +
    165E  ASP*     5.6     8.7    -      -       -      +
    168E  CYS*     4.0     8.3    -      -       -      -
    180E  MET*     1.3    73.7    -      -       -      +
    182E  CYS*     1.3    74.7    +      -       -      +
    183E  ALA*     3.9    12.6    -      -       +      -
    199E  VAL*     3.9    12.8    -      -       +      -
    210E  GLN*     3.4    23.8    -      -       +      -
    211E  GLY*     3.7    17.9    -      -       -      -
    227E  VAL*     3.6     3.4    -      -       -      -
    228E  TYR*     2.9    53.4    +      -       +      +
    229E  THR      3.8     6.1    -      -       -      -
    230E  LYS*     4.0    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 182 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163E  LEU*     2.9    49.5    +      -       +      +
    168E  CYS*     2.0    59.3    -      -       +      +
    172E  TYR*     4.3     2.7    -      -       -      -
    181E  PHE*     1.3    83.1    -      -       -      +
    183E  ALA*     1.3    56.3    +      -       -      +
    225E  PRO*     3.9    16.6    -      -       +      -
    226E  GLY      3.3     5.8    -      -       -      +
    227E  VAL*     4.0    17.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 183 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136E  CYS*     6.0     0.7    -      -       -      -
    138E  ILE*     4.6    10.5    -      -       +      -
    160E  ALA*     4.8     4.0    -      -       +      +
    161E  PRO      3.2    17.9    -      -       -      +
    162E  ILE*     4.3     2.9    -      -       +      -
    163E  LEU*     4.2     5.6    -      -       -      +
    181E  PHE*     3.9    13.0    -      -       +      -
    182E  CYS*     1.3    73.2    -      -       -      +
    184E  GLY*     1.3    59.2    +      -       -      +
    189E  ASP*     4.8     1.4    -      -       -      +
    199E  VAL*     5.1     3.8    -      -       +      -
    225E  PRO*     3.9     1.2    -      -       -      +
    226E  GLY      3.3    25.8    +      -       -      +
    228E  TYR*     3.6    29.4    +      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il